Why is my cube projection messed up in one scene but not the other?
Cube projection will project the mesh from 6 view directions ignoring the seams, and depends where the mesh located in 3D space and its rotation, UVs position will be calculated in UV/Image Editor.


  Blender offers several ways of mapping UVs. The simpler projection
  methods use formulas that map 3d space onto 2d space, by interpolating
  the position of points toward a point/axis/plane through a surface.
  The more advanced methods can be used with more complex models, and
  have more specific uses.


UV Mapping a Mesh